New model species for arctic-alpine plant molecular ecology
Abstract
Arctic and alpine, high latitude and high elevation environments are one of the most stressful environments for species to inhabit. This harshness manifests itself in lower species richness in comparison to more southern vegetation zones (Francis & Currie, 2003). Furthermore, the climatic oscillations—past and predicted—have the most dramatic effect on these ecosystems. For example, in regions of continental ice sheets—the northernmost part of Western Europe and North America—the Arctic species assemblages are no older than a few thousands of years, which is a relatively short period from an evolutionary perspective. Although similar environments may have existed further south during the Ice Age, allowing some preadaptation for the Arctic species, the current habitat is a unique combination of environmental factors such as the climate, soil, bedrock, and photoperiod. Hence, understanding the evolutionary forces shaping Arctic-alpine species will be important for predicting these vulnerable environments’ population viability and adaptive potential in the future. In this issue of Molecular Ecology Resources, Nowak et al. (Molecular Ecology Resources) present extensive genome-wide resources for an Arctic-alpine plant Draba nivalis. This adds a valuable new member into the cabbage family models for evolutionary genetics and adaptation studies, to accompany e.g., Arabidopsis (Nature Genetics, 43, 476; Nature, 408, 796), Arabis (Nature Plants, 1, 14023) and Capsella (Nature Genetics, 45, 831). A whole new avenue will open up for molecular ecological studies not only for D. nivalis, but the whole large Draba genus with its diverse ecological and evolutionary characteristics.
Draba nivalis is a self-compatible perennial plant with a Holarctic distribution (Figure 1). It belongs to a large genus of Draba, of whose 390 species typically inhabit Arctic-alpine, marginal, low-competition environments (Jordon-Thaden et al., 2013). For evolutionary genetic studies, the genus is biologically diverse with its large number of species containing variation in e.g., ploidy, mating system, and extent of distribution (Jordon-Thaden et al., 2013). D. nivalis itself is known to contain cryptic species (Grundt et al., 2006), thus facilitating speciation studies. Multiple evolutionary lineages allow joint analysis of adaptation, colonization and speciation processes and the new genomic resources will help to pinpoint the underlying molecular mechanisms.
The genomic resources published by Nowak et al. (2021) include genome assembly (302 Mb assembled into eight chromosomes), gene and transposable element annotation, linkage map, and information on polymorphic sites in the genome, to mention the focal resources. It is worth noting that a chromosome level assembly is still not simple to achieve, but greatly improves understanding the evolutionary forces shaping diversity that include linked selection and unequal distribution of genomic elements across chromosomes. In Nowak et al. (2021) a combination of Illumina short-reads, Nanopore long-reads, proximity ligation data, and linkage map from a cross between Norwegian and Alaskan strains resulted in a genome assembly of which contiguity and completeness is comparable with many Brassicaceae model species assemblies (Table 1). In particular, important steps for improving the assembly contiguity were the proximity ligation step (increased the scaffold N50 from 30 Kb to 2.9 Mb and decreased the scaffold L50 from 2663 to 30) and anchoring the scaffolds based on the linkage map (increased the scaffold N50 from 4.4 to 31 Mb).
| Species | Reference genome source & version | Special properties | Assembly size (Mb) | Number of scaffoldsa | Unknown bases (Mb) | Number of gaps | N50 (Mb) | L50 | Gene models | Original reference |
|---|---|---|---|---|---|---|---|---|---|---|
| Draba nivalis | Nowak et al. 2021 | Arctic-alpine distribution | 302 | 6648 | 20.67 | 21,877 | 34.19 | 5 | 33,537 | Nowak et al. (2021) |
| Aethionema arabicum | GoGe, v5_map_achored, genome id: 34234 | Representative of the basal Brassicaceae lineage | 196 | 2990b | 25.79 | 11,261 | 10.14 | 9 | 23,333 | Nguyen et al. (2019) |
| Arabidopsis lyrata | Phytozome V13, v2.1 | Local adaptation, hybrid incompatibility | 207 | 695 | 22.89 | 2953 | 24.46 | 4 | 31,073 | Hu et al. (2011); Rawat et al. (2015) |
| Arabidopsis thaliana | Phytozome V13, TAIR10 & Araport11 | Molecular genetics model species | 120 | 7c | 0.19 | 165 | 23.46 | 3 | 27,655 | The Arabidopsis Genome Initiative (2000); Cheng et al. (2017) |
| Arabis alpina | http://www.arabis-alpina.org/, V5 | Model for perenniality | 337 | 926 | 11.28 | 1856 | 36.6 | 4 | 34,220 | Willing et al. (2015); Jiao et al. (2017) |
| Capsella grandiflora | Phytozome V13, v1.1 | Self-incompatible relative of C. rubella, large effective population size | 105 | 4997 | 11.59 | 12,289 | 0.11 | 223 | 24,805 | Slotte et al. (2013) |
| Capsella rubella | Phytozome V12_unrestricted, 183_v1.0 | Recent shift to selfing | 135 | 853 | 4.76 | 8822 | 15.06 | 4 | 26,521 | Slotte et al. (2013) |
| Eutrema salsugineum | Phytozome V13, v.1.0 | Salt tolerance | 243 | 639 | 4.65 | 2872 | 13.44 | 8 | 26,351 | Yang et al. (2013) |
- a The assemblies did not include scaffolds shorter than 1000 bp except for A. arabicum.
- b Shortest scaffold 886 bp.
- c Only chromosomal scaffolds.
In addition to the genomic resources, Nowak et al. (2021) utilized three different approaches to investigate adaptive evolution signatures from the genome sequence of D. nivalis: (i) comparison of Pfam abundances across species, (ii) gene family composition analysis looking for significant expansions and contractions in Draba lineage, and (iii) identification of sites that have been subjects of positive selection in the branch leading to D. nivalis. These approaches were followed by gene ontology enrichment of the putatively selected loci to reveal processes, functions and cellular components specifically affected by positive selection. Ontology enrichment revealed multiple gene attributes that had either expanded in Draba lineage or experienced codon level selection pressure or both and deserve further empirical studies. For example, the enriched oxidation-reduction homeostasis and photoperiod related genes have indication of being especially important in Arctic-alpine environments. Interestingly, also meiosis related genes were identified as positively selected and significantly expanded in the Draba lineage, adding evidence that meiotic processes, despite being part of the essential machinery of the sexual reproduction, are sensitive to environmental conditions such as temperature (Bomblies et al., 2015).
All three methods of identifying adaptation signature applied to the D. nivalis genome are based on comparison to other, non-Draba species and thus cover evolutionary time of the entire Draba branch. This means probably over 10 million years of evolutionary history, much older than the existence of D. nivalis as a species and its history as an Arctic species. Investigating the species colonization and population split history in more detail will refine the existing framework of its adaptation. Population resequencing of different groups covering different parts of its distribution range will be technically straightforward with the help of reference genome published by Nowak et al. (2021). Resequencing data will allow identification of loci whose variants were favoured during the Arctic colonization, whether they are shared across the species distribution (putative preadaptation) or repeatedly adapted to similar environments independently. The utility of the D. nivalis reference genome expands to other Draba species and due to their distribution in multiple continents and different Arctic-alpine regions, allows studies of further patterns of convergent adaptation.
Another pivotal resource for selection studies is the information on recombination rate variation along the genome now available for D. nivalis. For example, the extent of linked selection depends on recombination rate variation which is important to take into account in population genetics selection inference (Charlesworth et al., 1993). Furthermore, variance in measures of differentiation, such as FST, was recently found to be correlated with recombination rate even in the absence of selection (Booker et al., 2020). Hence, incorporating recombination rate as a covariate in selection scans will decrease the false positive and false negative detections in regions of low and high recombination rate, respectively. The genomic resources for D. nivalis will facilitate comprehensive, less-biased investigations of adaptation genomics in this genus.
Unfortunately, Arctic-alpine vascular plants, including D. nivalis are predicted to experience serious range-contractions and even extinctions (e.g., Niskanen et al., 2019). Let's make sure that Draba spp. will not become model species of extinction genomics.
